Sureselect mouse all exon kit

Manufactured by Agilent Technologies

Sourced in United States

The SureSelect Mouse All Exon Kit is a targeted enrichment solution for capturing and sequencing the mouse exome. It provides comprehensive coverage of the mouse coding regions, enabling efficient and cost-effective whole-exome sequencing studies.

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Lab products found in correlation

Hiseq 2000, by Illumina (10 mentions) Paired end sample prep kit, by Illumina (3 mentions) Gentra puregene tissue kit, by Qiagen (3 mentions) Novaseq 6000, by Illumina (3 mentions) Picogreen, by Thermo Fisher Scientific (2 mentions) Prime phase lock gel heavy tubes, by Thermo Fisher Scientific (2 mentions) Proteinase k, by Meridian Bioscience (2 mentions) Hiseq 4000, by Illumina (2 mentions) Novaseq 6000 s4, by Illumina (1 mentions) Quick dna midiprep plus kit, by Zymo Research (1 mentions) Dneasy blood and tissue kit, by Qiagen (1 mentions) Solid 4, by Thermo Fisher Scientific (1 mentions) Mouse low density linkage panel, by Illumina (1 mentions) Eland, by Illumina (1 mentions) Nextseq, by Illumina (1 mentions) Dmem high glucose, by Merck Group (1 mentions) Hiseq x platform, by Illumina (1 mentions) Trueseq stranded mrna sample prep kit, by Illumina (1 mentions)

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SureSelect kits (5 citations) SureSelect Mouse Exon (3 citations)

23 protocols using sureselect mouse all exon kit

Whole Exome Sequencing and Variant Calling

Cited 1 time

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Whole exome sequencing was performed using the Agilent SureSelect mouse all exon kit. Captured material was indexed and sequenced on the Illumina GAII and HiSeq2000 platform at the Wellcome Trust Sanger Institute. Successfully sequenced reads were then aligned to mouse reference genome (GRCm38) followed by number of quality control routines (e.g. base quality score recalibration, realignment around InDels). We used Cake variants detection pipeline (Perna et al., 2015 (link); Rashid et al., 2013 (link)) to identify somatic as well as germline variants. A stringent variant caller overlapping strategy has been adapted to minimize false positive rate. Those detected by at least four of the five algorithms (embedded within Cake: Bambino; Varscan 2; Mpileup; SomaticSniper; Mutect) were subsequently filtered for depth, known mouse variations (Keane et al., 2011 (link)), strong germline activity and functional impact to produce a cleaner list of mutations (Table S1).

Sherborne A.L., Davidson P.R., Yu K., Nakamura A.O., Rashid M, & Nakamura J.L. (2015). Mutational analysis of ionizing radiation-induced neoplasms. Cell reports, 12(11), 1915-1926.

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Whole-Exome Sequencing of Colon Tumor Mice

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From each group, we selected 6 tumor-bearing mice to analyze by whole-exome sequencing (WES). For each mouse, tumor tissue was collected from a single tumor in the distal colon and matched normal tissue was collected from the proximal colon. Genomic DNA was isolated using the Quick-DNA Midiprep Plus Kit (Zymo Research) according to the manufacturer's instructions. Mouse exome libraries were prepared using the SureSelect Mouse All Exon Kit (Agilent) and samples were sequenced using an Illumina NovaSeq6000 S4.

Dougherty M.W., Valdés-Mas R., Wernke K.M., Gharaibeh R.Z., Yang Y., Brant J.O., Riva A., Muehlbauer M., Elinav E., Puschhof J., Herzon S.B, & Jobin C. (2023). The microbial genotoxin colibactin exacerbates mismatch repair mutations in colorectal tumors. Neoplasia (New York, N.Y.), 43, 100918.

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Exome Sequencing and Variant Analysis

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Sequencing was performed by the UTSW McDermott Center Next-Generation Sequencing Core, and data were analyzed by staff of the UTSW Bioinformatics Core Facility. In brief, exomes were captured with SureSelect Mouse All Exon Kit (Agilent, Santa Clara, CA), sequenced with ∼100× coverage, and variants were called with the Genome Analysis Toolkit (GATK) (75 (link)).

Xu P., Shimomura K., Lee C., Gao X., Simpson E.H., Huang G., Joseph C.M., Kumar V., Ge W.P., Pawlowski K.S., Frye M.D., Kourrich S., Kandel E.R, & Takahashi J.S. (2022). A missense mutation in Kcnc3 causes hippocampal learning deficits in mice. Proceedings of the National Academy of Sciences of the United States of America, 119(31), e2204901119.

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Somatic Variant Identification in Mouse Tumors

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DNA extraction was performed using the DNeasy Blood and Tissue Kit (Qiagen). Tumor and normal DNA samples were subjected to whole-exome sequencing (WES; SureSelect Mouse All Exon Kit, Agilent Technologies) at RUCDR Infinite Biologics (Piscataway, NJ). Paired-end sequencing data were aligned to the reference mouse genome mm10 using the Burrows-Wheeler Aligner (BWA, v0.7.15). Local realignment, duplicate removal and base quality score recalibration was performed using the Genome Analysis Toolkit (GATK, v3.1.1). After pooling the reads from each normal sample and masking repetitive regions using RepeatMasker (v4.0), somatic single nucleotide variants (SNVs) were identified using MuTect (v.1.1.4), and small insertions and deletions (indels) were detected using VarScan2 (v2.3.6) and Strelka (v3.1.1). To identify indels greater than 3 bp, Lancet, Platypus, and Scalpel were employed, and the results were combined to define a consensus call as previously described. SNVs and indels outside the WES capture were filtered out, as were SNVs and indels for which the variant allele fraction (VAF) in the tumor sample was less than 5 times the VAF of the paired normal tissue as previously described. Allele specific copy number aberrations (CNAs), tumor purity and ploidy were obtained from the WES data using FACETS.

Mahdi A.H., Huo Y., Chen Y., Selenica P., Sharma A., Merritt E., Barnard N., Chan C., Ganesan S., Reis-Filho J.S., Weigelt B., De S, & Xia B. (2020). Loss of the BRCA1-PALB2 interaction accelerates p53-associated tumor development in mice. Genes & Diseases, 9(3), 807-813.

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Neoantigen Identification Pipeline

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Whole exome sequencing was performed using the SureSelect Mouse All Exon kit (Agilent, 5190–4641). Libraries were sequenced on a Nextseq500 platform to a depth of 100X for tumor cell lines and 50x for normal germline tissue (150 bp PE reads). FASTQ reads passing QC were aligned to the mm10 reference genome using NextGenMap (Sedlazeck et al., 2013 (link)) (version 0.5.0). Duplicated reads were marked with Picard tools (version 2.17.4) and base recalibration performed with GATK (version 4.0). Somatic variants were identified using Mutect2 (GATK version 4.0) and Strelka2 (version 2.7.0) (Kim et al., 2017 ) annotated with SnpEff (version 4.3T). Variants were intersected and only variants called by both Mutect2 and Strelka2 were kept (Callari et al., 2017 (link)). Neoepitope prediction and MHC binding-affinity were calculated using the antigen.garnish R package (Rech et al., 2018 ). For MHC class I predictions, established median half-maximum inhibitory concentrations (IC50) of < 5,000nM or < 50nM were used to classify peptides as potential MHC binders or as CDNs, respectively. These cutoffs correspond to experimentally confirmed peptide-MHC binding and immunogenic CDN thresholds, respectively (Fritsch et al., 2014 (link); Paul et al., 2013 (link)).

Li J., Byrne K.T., Yan F., Yamazoe T., Chen Z., Baslan T., Richman L.P., Lin J., Sun Y.H., Rech A.J., Balli D., Hay C.A., Sela Y., Merrell A.J., Liudahl S.M., Gordon N., Norgard R.J., Yuan S., Yu S., Chao T., Ye S., Eisinger-Mathason T.S., Faryabi R.B., Tobias J.W., Lowe S., Coussens L.M., Wherry E.J., Vonderheide R.H, & Stanger B.Z. (2018). Tumor cell-intrinsic factors underlie heterogeneity of immune cell infiltration and response to immunotherapy. Immunity, 49(1), 178-193.e7.

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Exome Sequencing of Mouse Genome

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We used the SureSelect Mouse All Exon Kit (Agilent, Santa Clara, CA, USA) to enrich whole exons from genomic DNA of the G1 mouse. We performed resequencing using SOLiD4 (Life Technologies, Carlsbad, CA, USA) as reported previously
[32 (link)].

Arime Y., Fukumura R., Miura I., Mekada K., Yoshiki A., Wakana S., Gondo Y, & Akiyama K. (2014). Effects of background mutations and single nucleotide polymorphisms (SNPs) on the Disc1 L100P behavioral phenotype associated with schizophrenia in mice. Behavioral and Brain Functions : BBF, 10, 45.

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Exome Sequencing of ECM-resistant Mice

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27 mice from the Deric pedigree were genotyped with a panel of 196 polymorphic markers informative for the B6/B10 parental combination (Illumina Mouse Low Density Linkage panel), and genotypes were analyzed using the R/QTL software package using a binary phenotypic model. This analysis revealed linkage of ECM resistance to proximal Chr.19. Genomic DNA from 2 ECM-resistant Deric mice were subjected to whole-exome sequencing. Exome capture was performed using a SureSelect Mouse All Exon kit (Agilent Technologies) and parallel sequencing on an Illumina HiSeq 2000 (100-bp paired-end reads). Reads were aligned to mouse genome assembly July 2007 (NCBI37/mm9) with Burrows-Wheeler Alignment (BWA) tool (Li and Durbin, 2009 (link)) and coverage was assessed with BEDTools (Quinlan and Hall, 2010 (link)). Single nucleotide variants were called using samtools pileup and varFilter (Li and Durbin, 2009 (link)), and were then quality filtered to require at least 20% of reads supporting the variant call. Variants were annotated using Annovar (Wang et al., 2010 (link)) and custom scripts to identify whether they had previously been seen in mouse dbSNP128 or in any of 2 mouse exomes sequenced in parallel.

Kennedy J.M., Fodil N., Torre S., Bongfen S.E., Olivier J.F., Leung V., Langlais D., Meunier C., Berghout J., Langat P., Schwartzentruber J., Majewski J., Lathrop M., Vidal S.M, & Gros P. (2014). CCDC88B is a novel regulator of maturation and effector functions of T cells during pathological inflammation. The Journal of Experimental Medicine, 211(13), 2519-2535.

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Exome Sequencing of Tumor Samples

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Formalin-fixed or flash-frozen tumours free of visible normal tissue were digested overnight in proteinase K (Bioline) and phenol/chloroform purified using 5 PRIME Phase Lock Gel Heavy Tubes (Fisher Scientific). Integrity of genomic DNA was assessed by electrophoresis on 1% agarose gels, and concentration was determined by nanodrop spectrophotometry and PicoGreen (Invitrogen). Exome enrichment and sequencing genomic libraries were prepared using the Illumina Paired End Sample Prep Kit following manufacturer instructions. Enrichment was performed as described previously³² using the Agilent SureSelect Mouse All Exon kit following the manufacturer’s recommended protocol. Each exome was sequenced using a 76bp paired-end protocol on the Illumina platform (GAII or HiSeq2000).

Westcott P.M., Halliwill K.D., To M.D., Rashid M., Rust A.G., Keane T.M., Delrosario R., Jen K.Y., Gurley K.E., Kemp C.J., Fredlund E., Quigley D.A., Adams D.J, & Balmain A. (2014). The mutational landscapes of genetic and chemical models of Kras-driven lung cancer. Nature, 517(7535), 489-492.

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Exome Sequencing of Tumor Samples

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Screening for SARS-CoV-2 Resistant Mutations

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50 million of mutagenized haploid mSCs were infected with SARS-CoV-2 at a MOI of 5 in 5 ml of ES medium without FBS in 150 mm dish. One hour after infection, the cells were supplemented with complete ES medium and incubated at 37 °C with 5% CO₂. After outgrowth of virus-resistant cells, cell clones were picked separately and cultured. Resistance to SARS-CoV-2 was validated by infection with SARS-CoV-2. 5×10⁴ wild-type AN3–12 and potentially resistant clones cells per well (48-well plates) were seeded in complete ESCell medium. Four hours post seeding, cells were infected with SARS-CoV-2 at a MOI of 5 and checked for cell survival for a week. All clones resistant to SARS-CoV-2 infection were subjected to DNA extraction using the Gentra Puregene Tissue Kit (Qiagen). Paired end, 150 bp whole exome sequencing was performed on an Illumina Novaseq 6000 instrument after precapture-barcoding and exome capture with the Agilent SureSelect Mouse All Exon kit. For data analysis, raw reads were aligned to the reference genome mm9. Variants were identified and annotated using GATK and snpEff. CCHFV resistance causing alterations were identified by allelism only considering variants with moderate or high effect on protein and a read coverage >20.

Monteil V., Kwon H., John L., Salata C., Jonsson G., Vorrink S.U., Appelberg S., Youhanna S., Dyczynski M., Leopoldi A., Leeb N., Volz J., Hagelkruys A., Kellner M.J., Devignot S., Michlits G., Foong-Sobis M., Weber F., Lauschke V.M., Horn M., Feldmann H., Elling U., Penninger J.M, & Mirazimi A. (2023). Identification of CCZ1 as an essential lysosomal trafficking regulator in Marburg and Ebola virus infections. Nature Communications, 14, 6785.

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